In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision.

ABSTRACT:

Background

High-throughput sequencing can establish the functional capacity of a microbial community by cataloging the protein-coding sequences (CDS) present in the metagenome of the community. The relative performance of different computational methods for identifying CDS from whole-genome shotgun sequencing is not fully established.

Results

Here we present an automated benchmarking workflow, using synthetic shotgun sequencing reads for which we know the true CDS content of the underlying communities, to determine the relative performance (sensitivity, positive predictive value or PPV, and computational efficiency) of different metagenome analysis tools for extracting the CDS content of a microbial community. Assembly-based methods are limited by coverage depth, with poor s

SUBMITTER: Golob JL 

PROVIDER: S-EPMC7559173 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature